Objective This study aimed to examine the metabolising effect of chrysin by investigating the mRNA expression levels of PPAR alpha and its related cellular mechanisms in HCT116 cells. Results The mRNA expression of PPAR alpha was significantly induced in HCT116 cells following treatment with chrysin for 36 h, but the mRNA expression of PPAR alpha was inhibited, when the cells were treated with a combination of chrysin and MK886 (PPAR alpha inhibitor). This phenomenon proved that the incorporation of MK886 lowers the expression levels of PPAR alpha, thus enabling us to study the function of PPAR alpha. The cell population of the G0/G1 phase significantly increased in chrysin-treated cells, which was accompanied by a decrease in the percentage of S phase cell population after 12 h of treatment. However, treatments of HCT116 cells with chrysin only or a combination of chrysin and MK886 did not show the opposite situation in the G0/G1 and S phase cell populations, indicating that the expression of PPAR alpha may not be associated with the cell cycle in the treated cells. The migration rate in chrysin-treated HCT116 cells was reduced significantly after 24 and 36 h of treatments. However, the activity was revived, when the expression of PPAR alpha was inhibited, indicating that the migration activity of chrysin-treated cells is likely correlated with the expression of PPAR alpha. Comparison of the CYP2S1 and CYP1B1 mRNA expression in chrysin only treated, and a combination of chrysin and MK886-treated HCT116 cells for 24 and 36 h showed a significant difference in the expression levels, indicating that PPAR alpha inhibitor could also modify the expression of CYP2S1 and CYP1B1. Conclusion The study indicates that PPAR alpha may play an essential role in regulating the migration activity, and the expression of CYP2S1 and CYP1B1 in chrysin-treated colorectal cancer cells.